In silicochromosome staining

The chromosomal bands observed upon Giemsa staining are thought to correspond generally to regions that are GC-poor (Giemsa-dark, G bands) and GC-rich (Giemsa-light, R bands). The exact relationship between sequence base composition and cytogentic banding is still unclear, however. In the January 22 Proceedings of the National Academy of Sciences, Niimura and Gojobori describe a computational method to explore the association between the Giemsa banding pattern and local GC content (Proc Natl Acad Sci USA 2002, 99:797-802). They began with human chromosomes 21 and 22 and developed a 'two-window analysis' method to investigate GC content compared to flanking regions. Using a local window of 2.5 Mb and a regional window of 9.3 Mb, they were able to create an in silico banding pattern that resembled Giemsa staining. They extended their in silicostaining method to the whole human genome and demonstrate impressive accuracy in predicting Giemsa-dark bands.